Welcome to John Pandolfi’s Lab at The University of Queensland

Recent funding for ‘Managing regime shifts and fisheries collapse on the Great Barrier Reef – the role of ancient DNA’ was awarded from BGI Australia’s call for proposals on new research involving genomic applications in biodiversity and evolution.

This research project will allow us to gain insight into the palaeoecology of reef organisms that do not leave a substantial fossil record by analyzing the ancient environmental DNA that has been preserved in the marine sediment.

In collaboration with BGI Australia and the Riginos lab at UQ, we will reconstruct past occurrences of several important reef organisms, including macro-algae and fish, over a gradient of increasing human impact.

Centuries-old nautical charts, mapped by long-deceased sailors to avoid shipwrecks, have been used by modern scientists to study loss of coral reefs. A new US and Australian study – including research from The University of Queensland and the Australian Research Council Centre of Excellence in Coral Reef Studies – compared early British charts to modern coral habitat maps to understand changes to reef environments.

UQ’s Professor John Pandolfi said the study used information from surprisingly accurate 18th century nautical charts and satellite data to understand coral loss over more than two centuries in the Florida Keys. “We found that some reefs had completely disappeared,” Professor Pandolfi said.

The study was led by Loren McClenachan, Assistant Professor at Colby College, in Waterville, Maine, USA. Professor McClenachan said more than half of the coral reef habitat mapped in the 1770s was no longer there. In some areas, particularly near land, coral loss was closer to 90 per cent. “We found near the shore, entire sections of reef are gone, but in contrast, most coral mapped further from land is still coral reef habitat today,” she said. This estimate of change over centuries added to modern observations of recent loss of living corals.

The marine scientists measured the loss of coral reef habitats across a large geographic area, while most studies look more closely at the loss of living coral from smaller sections of the reef. “We found that reef used to exist in areas that today are not even classified as reef habitat anymore,” Professor Pandolfi said. “When you add this to the 75 per cent loss of living coral in the Keys at that finer scale, the magnitude of change is much greater than anyone thought.”

This work was undertaken while Professor McClenachan was a visiting researcher in Professor Pandolfi’s lab at UQ’s School of Biological Sciences in Brisbane, Australia, while on sabbatical from Colby College. The research revealed the precision of the early maps. Postdoctoral researcher at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine Dr Benjamin Neal said the early chart makers represented the “Silicon Valley of their time”. “They had the best technology and they used it to create new information that conferred a lot of power,” Dr. Neal said. “The maps were essential to expansion of the British Empire, and luckily for us, they also included a lot of useful ecological information.”

Professor McClenachan said the findings had important conservation implications and pointed to a shifted spatial baseline. “We tend to focus on known areas where we can measure change. That makes sense. Why would you look for coral where you never knew it was?” she said.

The authors said when large-scale changes like this were overlooked, scientists could lose sight of past abundance, lowering expectations for conservation and recovery.

The study, which also involved authors from Columbia University, National Museum of Natural History, Smithsonian Institution and the University of California San Diego, all in the U.S., is published in Science Advances (doi: 10.1126/sciadv.1603155)

Coral range expansions would likely vary among species depending on the species’ characteristics and traits.

“In the subtropical-to-temperate transition zone south of the Great Barrier Reef, corals are at the limits of their distribution and environmental tolerances, as the water is cooler,” Dr Sommer said.

“There is less light and conditions are more seasonal and variable than on the Great Barrier Reef.”

Dr Sommer, a member of Professor John Pandolfi’s lab at UQ, said the new study examined 17 reefs from the Sunshine Coast, in south-east Queensland, to Port Stephens in New South Wales.

“We sought to investigate the ecological and evolutionary processes that shape coral biodiversity patterns at their southern range limits,” she said.

“We also examined the evolution of coral species’ traits to determine whether these characteristics were stable over time.”

Dr Sommer said it was important to conduct such studies to understand the stability of the species’ environmental tolerances and the ecological drivers of biodiversity patterns so scientists could more accurately predict species’ range shifts and ecological responses to climate change.

“For example, if characteristics such as environmental tolerances are stable over time and don’t change, then corals will likely only expand their ranges to areas where environmental conditions are similar to where corals currently occur,” Dr Sommer said.

“And corals will probably have less capacity to adapt to novel environmental conditions”.

“Our results suggest that species that occur in these subtropical and temperate reefs south of the Great Barrier Reef are more closely related to each other and have more similar characteristics than the coral species that occur on the Great Barrier Reef.

“This suggests that environmental tolerance is important for coral persistence in these marginal environments and that species with unsuitable traits cannot persist in these cooler and more light-limited environments.”

Results suggested competition by corals for space and light were also important drivers of biodiversity patterns at local scales.

“These findings indicate that coral biodiversity patterns south of the Great Barrier Reef are shaped by a combination of regional and local processes,” Professor Pandolfi said.

Species unable to persist in these cooler and darker conditions were initially excluded from the region and the remaining species then divided into local sites, depending on whether species interactions or environmental conditions were more important locally.

The study, which involved researchers from the Australian Research Council Centre of Excellence for Coral Reef Studies, the ARC Centre of Excellence for Environmental Decisions at UQ, University of Leeds, Southern Cross University and CSIRO Marine and Atmospheric Research, is published in the Proceedings of the Royal Society B.

An opportunity has become available to apply for a PhD scholarship jointly held with the University of Queensland, Australia and the University of Exeter, UK.

We are looking for a candidate with a strong academic background and track record, with an interest in pursuing historical marine ecology research. If successful, the candidate’s home institution will be the University of Queensland, but they will spend time at both UQ and the University of Exeter (Falmouth campus) and will receive a joint degree from the two institutions. PhDs will be awarded on a competitive basis and candidates need to complete an expression of interest form on the below website by 11th September 2017 (note the short turnaround).

Further information on the application process can be found at https://global-engagement.uq.edu.au/quex. Successful candidates will receive a living stipend, tuition fees, and funds for travel and training.

We are excited to announce that we have a number of new PhD and Post-Doctoral researchers starting in the Pandolfi lab this year.

Steve Dalton is a post-doctoral researcher in the School of Biological Sciences University of Queensland, but situated at the National Marine Science Centre in Coffs Harbour. Steve has extensive knowledge of marine habitats along the NSW and southern QLD coastline. He is currently undertaking research focussed on assessing the potential for tropical coral species migration to higher latitudes and understanding the mechanisms that enable warm water coral specialist to grow and persist at marginal reefs along the eastern seaboard. This work aims to assess the influence of elemental stoichiometry in corals and their symbionts in determining how changes in metabolic rates might define latitudinal limits in the distribution of reef corals.

Nataly Gutierre Isaza comes to us from Colombia where she completed her Bachelors in biology, and she completed her Masters in Natural Resources and Rural Development in Mexico. She has an interest in reef dynamics and competition between hard corals and macroalgae, the causes of coral reef degradation as well as the traits involved in coral species adaptation to novel environmental conditions imposed by climate change.

Her PhD will focus on the ecological stoichiometry of coral larvae along the latitudinal gradient in eastern Australia. For more information see Nataly’s profile.

Karin Zwiep has returned to the Pandolfi lab to undertake her PhD after an eight-month research visit during her masters. Karin completed her masters of environmental biology and bachelor in biology at Utrecht University, Holland. She has been involved in research projects from crustacean-ciliate symbioses in Dutch waters to dinoflagellate cysts and pollen in the Mediterranean sapropels, as well as genetic diversity and connectivity of Symbiodinium in high latitude reefs along the Australian coast.

Her current PhD project will work on community structure changes and phase shifts of coral reef ecosystems using ancient DNA. For more information see Karin’s profile.

Marine Palaeoecology lab members have recently returned from the ARC Centre of Excellence for Coral Reef Studies – Coral Reef Futures Symposium held at the Shine Dome in Canberra on the 15th and 16th June, 2017. The Symposium featured more than 30 presentations from leading international marine scientists from the ARC Centre of Excellence, Exeter University, WorldFish, and the Great Barrier Reef Marine Park Authority, as well as a Public Forum hosted by none other than Dr Karl.

The coral reef futures title of the symposium invoked the findings of the recently released Nature paper by Hughes and colleagues that coral reefs can no longer return to their former glory due to the multitude of pressures they face, especially from global warming. Instead, important ecosystem processes and functions must be maintained to conserve healthy functioning reefs, and “the way forward is for research to inform and support reef governance and management to navigate the transition to new ecosystems that will maintain biodiversity, biological functions and support human well-being”.

Lab leader Professor John Pandolfi presented the findings of the sub-tropical bleaching surveys undertaken in April 2016 to assess bleaching extent and October 2016 to assess mortality and recovery. Comparing findings with those from the Great Barrier Reef (GBR) he showed the coral genera impacted by bleaching in the sub-tropics differed to those genera along the GBR. See Professor Pandolfi’s talk here.

A complex and increasing range of environmental and legal policy initiatives have been established to conserve biodiversity by improving management of human activities and their impacts on marine environments. These policies include international agreements, laws and conventions along with those at the national and local level, and span many sectors including conservation, fisheries, and agriculture. Despite this array of policies, along with international and national levels of protection, the condition of Australia’s Great Barrier Reef continues to deteriorate. This trend indicates that policies are inadequate or the right policies have been prescribed but not effectively implemented.

With colleagues from the ARC Centre of Excellence for Coral Reef Studies and the University of Queensland, I determined what policies influenced on-ground management of the Great Barrier Reef World Heritage Area and Marine Park and how these policies were implemented. Further, we identified challenges facing practitioners when applying these policies. In undertaking this research, 19 key informant interviews were conducted across Commonwealth and state jurisdictions and agencies involved in managing the Marine Park, and extensive content analysis of policy instruments relevant to the Great Barrier Reef was undertaken.

Effective policy implementation is a challenging task, limited by gaps between intentions and outcomes, inconsistencies, and conflicting agendas. Identifying how policies are put into practice and their efficacy should lead to improved understanding of whether the intent of international agreements, Commonwealth, and state policy is being realised, and whether this is impacting the ability of on-ground management to deliver effective outcomes for biodiversity.

A new study has ingeniously reconstructed a 103-year record of the Queensland east coast Spanish Mackerel spawning fishery, and revealed that catch rates have declined by 70 per cent over the past 80 years. The ARC Centre of Excellence for Coral Reef Studies and University of Queensland study documented the decline by combining data from historical newspapers with fisher memories.

Lead author and UQ PhD graduate Dr Sarah Buckley of the Sea-Fisheries Protection Authority in Ireland said the decline has had substantial consequences. “For the past 20 years the Cairns fishery has been commercially extinct and the Townsville spawning aggregations have remained completely offshore,” she said.

Co-author Professor John Pandolfi of UQ’s School of Biological Sciences and the ARC Centre of Excellence for Coral Reef Studies at UQ said the conservation of spawning aggregations of fish was one of a suite of management tools that could contribute to healthy fish populations. “Managers need to consider increased protection of Spanish Mackerel during this critical time if it is hoped that catch rates can be increased,” Professor Pandolfi said.

Spanish Mackerel are large and important recreational and commercial fish found in Queensland and northern New South Wales waters. Annually they form huge aggregations for breeding purposes at discrete locations for a confined period of time in the Great Barrier Reef. Although this fishery commenced over 100 years ago, official commercial catch and effort were not recorded by the government until the 1980s, leaving large gaps in our understanding of long-term changes in the fish spawning aggregations, some of which disappeared undetected. The scientists interviewed commercial fishers about their memories of changes to catch, gear and technology and locations fished, to reconstruct a valuable and comprehensive record.

Co-author Dr Ruth Thurstan of Deakin University said Spanish Mackerel fishers were able to recall fishing from as early as the 1940s, providing a wealth of knowledge that could be used to plug these historical data gaps. Preventing decline and loss of fish spawning aggregations is a priority for the Great Barrier Marine Park Authority. These data are currently being used by the Queensland government to inform stock assessment, demonstrating the valuable knowledge that is held by long-term fishers and in our local archives.

Climate-driven change in the distribution of animal and plant species poses emerging challenges for humans, an international study has shown. University of Queensland marine biologist Professor John Pandolfi said species were changing their distributions globally in response to climate change. “New challenges for humans range from health risks to economic threats, and from conflict over fisheries resources to impacts on the supply of coffee and other crops,” said Professor Pandolfi, of UQ’s School of Biological Sciences.

The study involved a large international team of scientists, led by Associate Professor Gretta Pecl from the University of Tasmania’s Institute for Marine and Antarctic Studies. The team’s report said species are already responding to climate change, and human communities and economies from the tropics to the poles are affected.

Conservation ecologist Dr Justine Shaw(pictured) of UQ’s School of Biological Sciences and the ARC Centre of Excellence for Environmental Decisions said species “in Antarctica, the Arctic, the tropics, everywhere” were moving in response to climate change. “This study shows just how valuable long-term monitoring is,” she said. “It allows us to detect these changes, particularly in rapidly warming areas like Antarctica and the Arctic.”

Associate Professor Pecl said human survival depended on other life on earth so the redistribution of the planet’s living organisms was a substantial challenge for people worldwide. “As their local environment changes, many plants and animals are responding by moving to higher altitudes, greater depths in the oceans, or towards the poles,” she said. “Previous studies have shown that land-based species are moving polewards by an average of 17km per decade, and marine species by 72km per decade. “Our study demonstrates how these changes are affecting worldwide ecosystems and human health and culture in the process. “While some species favour a warmer climate and are becoming more abundant, many others that humans exploit or interact with face depletion or extinction.”

Dr Pecl said that as humans relied on natural ecosystems for food, industry, health and culture, they were affected by changes in species distribution in many different ways. “These include resources, such as fish, forests and crops, which are at risk as their environments change. “The principal coffee-growing regions are expected to shift, and valuable timber species such as Norway spruce are expected to make way for less valuable, warm climate species. In industry, tourism and recreational fishing are jeopardised as corals die, jellyfish infest waters used for recreation, and urchins destroy fish habitats in kelp forests. Human conflict could escalate, as tensions emerge and species move between economic zones, as with Iceland’s ‘mackerel wars’, or due to disputes over competing land uses. Health threats such as malaria are becoming more prevalent as rising temperatures allow the poleward spread of mosquitos into regions where people have not had prior exposure.”

University of Queensland researchers are part of a team that will conduct Great Barrier Reef aerial and underwater surveys this month as coral bleaching occurs for the second year in a row. The work coincides with a report in the journal Nature today, which says the reef’s resilience is waning rapidly.

UQ School of Biological Sciences researcher Professor John Pandolfi said scientists from UQ and other institutions would compare the extent of coral bleaching damage that had occurred this summer with that of last summer. Professor Pandolfi is one of 46 researchers who contributed to the Nature report.

He said coral bleaching events should not be seen as individual disturbances to reefs, but as recurring events that threatened the viability of coral reefs globally. “We have known for some time that ‘refuge’ areas nearby help reef coral rebound after a bleaching event, but last year’s bleaching has shown that unfortunately this ability breaks down as bleaching becomes more severe,” Professor Pandolfi said.

The newly published research was led by ARC Centre of Excellence for Coral Reef Studies Director Professor Terry Hughes, at James Cook University. Professor Hughes said the research team hoped temperatures would drop quickly in the next two to three weeks, and this year’s bleaching would not be as severe as in 2016. “The severity of the 2016 bleaching was off the chart,” he said. “It was the third major bleaching to affect the Great Barrier Reef, following earlier heatwaves in 1998 and 2002. Now we’re gearing up to study a potential number-four.”

The research found that in 2016 catastrophic levels of bleaching occurred in the northern third of the reef, a region about 800km long. Professor Pandolfi said coral bleaching occurred when abnormal environmental conditions such as high sea temperatures caused corals to expel tiny photosynthetic zooxanthellae algae. “The loss of these colourful algae causes the corals to turn white,” he said. “Bleached corals can recover if the temperature drops and zooxanthellae are able to recolonise them. Otherwise the coral may die.”